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- PDB-1t0w: 25 NMR structures of Truncated Hevein of 32 aa (Hevein-32) comple... -

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Basic information

Entry
Database: PDB / ID: 1t0w
Title25 NMR structures of Truncated Hevein of 32 aa (Hevein-32) complex with N,N,N-triacetylglucosamina
ComponentsHevein
KeywordsSUGAR BINDING PROTEIN / alpha-helix / anti-parallel beta-sheet
Function / homology
Function and homology information


chitin binding / RNA nuclease activity / defense response to fungus / defense response to bacterium
Similarity search - Function
Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. ...Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / RlpA-like domain superfamily
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Pro-hevein
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsAboitiz, N. / Vila-Perello, M. / Groves, P. / Asensio, J.L. / Andreu, D. / Canada, F.J. / Jimenez-Barbero, J.
Citation
Journal: Chembiochem / Year: 2004
Title: NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides
Authors: Aboitiz, N. / Vila-Perello, M. / Groves, P. / Asensio, J.L. / Andreu, D. / Canada, F.J. / Jimenez-Barbero, J.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: The interaction of hevein with N-acetylglucosamine-containing oligosaccharides. Solution structure of hevein complexed to chitobiose
Authors: Asensio, J.L. / Canada, F.J. / Bruix, M. / Rodriguez-Romero, A. / Jimenez-Barbero, J.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from amaranthus caudatus
Authors: Martins, J.C. / Maes, D. / Loris, R. / Pepermans, H.A. / Wyns, L. / Willem, R. / Verheyden, P.
#3: Journal: Glycobiology / Year: 1998
Title: NMR investigations of protein-carbohydrate interactions: refined three-dimensional structure of the complex between hevein and methyl beta-chitobioside
Authors: Asensio, J.L. / Canada, F.J. / Bruix, M. / Gonzalez, C. / Khiar, N. / Rodriguez-Romero, A. / Jimenez-Barbero, J.
#4: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2000
Title: NMR Investigations of Protein-Carbohydrate Interactions: Studies on the Relevance of Trp/Tyr Variations in Lectin Binding Sites as Deduced from Titration Microcalorimetry and NMR Studies on ...Title: NMR Investigations of Protein-Carbohydrate Interactions: Studies on the Relevance of Trp/Tyr Variations in Lectin Binding Sites as Deduced from Titration Microcalorimetry and NMR Studies on Hevein Domains. Determination of the NMR Structure of the Complex between Pseudohevein and N'N',N''-triacetylchitotriose
Authors: Asensio, J.L. / Siebert, H.-C. / von der Lieth, C.-W. / Laynez, J. / Bruix, M. / Soedjanaamadja, U.M. / Beintema, J.J. / Canada, F.J. / Gabius, H.-J. / Jimenez-Barbero, J.
#5: Journal: Chem.Biol. / Year: 2000
Title: Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains
Authors: Asensio, J.L. / Canada, F.J. / Siebert, H.-C. / Laynez, J. / Poveda, A. / Nieto, P.M. / Soedjanaamadja, U.M. / Gabius, H.-J. / Jimenez-Barbero, J.
History
DepositionApr 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hevein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1122
Polymers3,4851
Non-polymers6281
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 25all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Hevein / ALLERGEN HEV B 6


Mass: 3484.858 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Source method: obtained synthetically
Details: Sequence prepared on a MBHA resin by standard solid phase peptide synthesis protocols. The SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HEVEA BRASILIENSIS (PARA RUBBER TREE).
References: UniProt: P02877
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques at tm = 200 and 300 ms

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Sample preparation

DetailsContents: 0.5 mM hev32, 3 mM chitotriose, 20 mM phosphate buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionClassification
XwinNMR3.2collection
XEASY1.3.13data analysis
DIANA1.5structure solution
Amber5refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 339 restraints: 321 are NOE-derived distance constraints and 18 come from cys-cys disulfide bridges
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 25 / Conformers submitted total number: 25

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